ArticleScientific reports2025
Evaluation of variability in cell-free DNA extraction efficiency from plasma and urine and spike-in normalization.
Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
5 citing papers in PubMed.
- Urinary DNA Extraction in Uro-Oncology and Selected Non-Urological Malignancies: A Narrative Review.Journal of clinical medicine · 2026Review
- Evaluating effects of tissue type, preservation method, and decomposition on DNA quality to support genetic sampling in stranded small cetaceans.Scientific reports · 2026Article
- Proof of concept for aqueous two-phase system-based extraction of cell-free DNA from plasma for liquid biopsy applications.Scientific reports · 2026Article
- Harmonising ctDNA Measurement in Haematological Malignancies: Traceability, Commutability and Reporting.Diagnostics (Basel, Switzerland) · 2026Review
- Variability and longitudinal dynamics of donor-derived cell-free DNA in kidney and liver recipients: a comparison of absolute and relative quantities in plasma and urine.Frontiers in transplantation · 2026Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Cell-free DNA (cfDNA) is a promising new biomarker for clinical use in e.g. oncology and transplantation medicine. Urinary cfDNA is also gaining interest as a non-invasive biomarker. However, cfDNA extraction is not standardised, leading to a variety of different methods being used with varying efficiencies and size-specificities. In this study, we aimed to assess the variability in cfDNA extraction efficiency for multiple cfDNA extraction methods (QIAamp Circulating Nucleic Acid Kit, Zymo Quick-DNA Urine Kit, Q Sepharose protocol (Qseph)) using the artificial spike-in CEREBIS and compare the contribution of variable extraction efficiency to overall variability in cfDNA quantities determined using droplet digital PCR (ddPCR). We found reproducible extraction efficiencies specific for each method with 84.1% (± 8.17) in plasma, 58.7% (± 11.1) for Zymo, as well as 30.2% (± 13.2) for Qseph based on the 180 bp CEREBIS (Construct to Evaluate the Recovery Efficiency of cfDNA extraction and BISulphite modification) spike-in. Additionally, while the largest proportion of the technical variability was observed between extractions, it was almost negligible compared to the biological variability. Normalization of urinary cfDNA using creatinine in urine reduced the variability, whereas when normalizing for CEREBIS-based extraction efficiency this was not consistently observed. With overall relatively consistent extraction efficiencies within each cfDNA extraction method, normalization for extraction efficiency using CEREBIS thus did not show a clear benefit but might be considered for comparisons between extraction methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.